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<title>GenomeTools - manual page for GT-SEED_EXTEND(1)</title>
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<div class="sect1">
<h2 id="_name">NAME</h2>
<div class="sectionbody">
<div class="paragraph"><p>gt-seed_extend - Calculate local alignments using the seed and extend algorithm.</p></div>
</div>
</div>
<div class="sect1">
<h2 id="_synopsis">SYNOPSIS</h2>
<div class="sectionbody">
<div class="paragraph"><p><strong>gt seed_extend</strong> [option &#8230;] encseq_basename [encseq_basename]</p></div>
</div>
</div>
<div class="sect1">
<h2 id="_description">DESCRIPTION</h2>
<div class="sectionbody">
<div class="dlist"><dl>
<dt class="hdlist1">
<strong>-ii</strong> [<em>string</em>]
</dt>
<dd>
<p>
Input index for encseq encoded sequences
</p>
</dd>
<dt class="hdlist1">
<strong>-qii</strong> [<em>string</em>]
</dt>
<dd>
<p>
Query input index (encseq)
</p>
</dd>
<dt class="hdlist1">
<strong>-seedlength</strong> [<em>value</em>]
</dt>
<dd>
<p>
Minimum length of a seed
default: logarithm of input length with alphabet size as log-base
</p>
</dd>
<dt class="hdlist1">
<strong>-spacedseed</strong> [<em>value</em>]
</dt>
<dd>
<p>
use spaced seed of length specified by option -seedlength
(optional argument specifies  weight of spaced seed) (default: 0)
</p>
</dd>
<dt class="hdlist1">
<strong>-diagbandwidth</strong> [<em>value</em>]
</dt>
<dd>
<p>
Logarithm of diagonal band width in the range
from 0 to 10 (for filter) (default: 6)
</p>
</dd>
<dt class="hdlist1">
<strong>-mincoverage</strong> [<em>value</em>]
</dt>
<dd>
<p>
Minimum coverage in two neighbouring diagonal bands (for filter)
default: 2.5 x seedlength
</p>
</dd>
<dt class="hdlist1">
<strong>-diagband-stat</strong> [<em>&#8230;</em>]
</dt>
<dd>
<p>
Compute statistics from diagonal band scores; parameter specifies kind of statistics, possible choices are
sum (default: sum)
</p>
</dd>
<dt class="hdlist1">
<strong>-maxfreq</strong> [<em>value</em>]
</dt>
<dd>
<p>
Maximum frequency of a k-mer (for filter) (default: undefined)
</p>
</dd>
<dt class="hdlist1">
<strong>-memlimit</strong> [<em>string</em>]
</dt>
<dd>
<p>
Maximum memory usage to determine the maximum frequency of a k-mer (for filter) (default: undefined)
</p>
</dd>
<dt class="hdlist1">
<strong>-extendxdrop</strong> [<em>value</em>]
</dt>
<dd>
<p>
Extend seed to both sides using xdrop algorithm,
optional parameter specifies sensitivity (default: 97)
</p>
</dd>
<dt class="hdlist1">
<strong>-xdropbelow</strong> [<em>value</em>]
</dt>
<dd>
<p>
Specify xdrop cutoff score (0 means automatically defined depending on minidentity)
</p>
</dd>
<dt class="hdlist1">
<strong>-extendgreedy</strong> [<em>value</em>]
</dt>
<dd>
<p>
Extend seed to both sides using greedy algorithm,
optional parameter specifies sensitivity (default: 97)
</p>
</dd>
<dt class="hdlist1">
<strong>-maxmat</strong> [<em>value</em>]
</dt>
<dd>
<p>
compute maximal matches of minimum length specified by option -l (default: 1)
</p>
</dd>
<dt class="hdlist1">
<strong>-l</strong> [<em>value</em>]
</dt>
<dd>
<p>
Minimum length of aligned sequences  (default: undefined)
</p>
</dd>
<dt class="hdlist1">
<strong>-minidentity</strong> [<em>value</em>]
</dt>
<dd>
<p>
Minimum identity of matches (for seed extension) (default: 80)
</p>
</dd>
<dt class="hdlist1">
<strong>-evalue</strong> [<em>value</em>]
</dt>
<dd>
<p>
switch on evalue filtering of matches (optional argument specifies evalue threshold) (default: 10.000000)
</p>
</dd>
<dt class="hdlist1">
<strong>-outfmt</strong> 
</dt>
<dd>
<p>
specify what information about the matches to display
alignment:        show alignment (possibly followed by
                  =&lt;number&gt; to specify width of alignment
                  columns, default is )
seed_in_algn:     mark the seed in alignment
polinfo:          add polishing information for shown
                  alignment
seed:             abbreviation for seed.len seed.s seed.q
failed_seed:      show the coordinates of a seed extension,
                  which does not satisfy the filter conditions
fstperquery:      output only the first found match per query
tabsep:           separate columns by tabulator, instead of
                  space as default
blast:            output matches in blast format 7 (tabular with
                  comment lines; instead of gap opens, indels are
                  displayed)
gfa2:             output matches in gfa2 format
custom:           output matches in custom format, i.e. no
                  columns are pre-defined; all columns have to be
                  specified by the user
cigar:            display cigar string representing alignment
                  (no distinction between match and mismatch)
cigarX:           display cigar string representing alignment
                  (distinction between match (=) and mismatch
                  (X))
trace:            display trace, i.e. a compact representation
                  of an alignment (possibly followed by =&lt;delta&gt;)
                  to specify the delta-value; default value of
                  delta is 50
dtrace:           display trace as differences; like trace, but
                  instead of an absolute value x, report the
                  difference delta-x. This leads to smaller
                  numbers and thus a more compact representation
s.len:            display length of match on subject sequence
s.seqnum:         display sequence number of subject sequence
subject id:       display sequence description of subject
                  sequence
s.start:          display start position of match on subject
                  sequence
s.end:            display end position of match on subject
                  sequence
strand:           display strand of match using symbols F
                  (forward) and P (reverse complement)
q.len:            display length of match on query sequence
q.seqnum:         display sequence number of query sequence
query id:         display sequence description of query
                  sequence
q.start:          display start position of match on query
                  sequence
q.end:            display end position of match on query
                  sequence
alignment length: display length of alignment
mismatches:       display number of mismatches in alignment
indels:           display number of indels in alignment
gap opens:        display number of indels in alignment
score:            display score of match
editdist:         display unit edit distance
identity:         display percent identity of match
seed.len:         display length seed of the match
seed.s:           display start position of seed in subject
seed.q:           display start position of seed in query
s.seqlen:         display length of subject sequence in which
                  match occurs
q.seqlen:         display length of query sequence in which
                  match occurs
evalue:           display evalue
bit score:        display bit score
</p>
</dd>
<dt class="hdlist1">
<strong>-ani</strong> [<em>yes|no</em>]
</dt>
<dd>
<p>
output average nucleotide identity determined from the computed matches (which are not output) (default: no)
</p>
</dd>
<dt class="hdlist1">
<strong>-no-reverse</strong> [<em>yes|no</em>]
</dt>
<dd>
<p>
do not compute matches on reverse complemented strand (default: no)
</p>
</dd>
<dt class="hdlist1">
<strong>-no-forward</strong> [<em>yes|no</em>]
</dt>
<dd>
<p>
do not compute matches on forward strand (default: no)
</p>
</dd>
<dt class="hdlist1">
<strong>-use-apos</strong> [<em>yes|no</em>]
</dt>
<dd>
<p>
Discard a seed only if both apos and bpos overlap with a previous successful alignment (default: no)
</p>
</dd>
<dt class="hdlist1">
<strong>-parts</strong> [<em>value</em>]
</dt>
<dd>
<p>
Divide data into specified number of parts (default: 1)
</p>
</dd>
<dt class="hdlist1">
<strong>-kmerfile</strong> [<em>yes|no</em>]
</dt>
<dd>
<p>
Use pre-calculated k-mers from file (if exist) (default: yes)
</p>
</dd>
<dt class="hdlist1">
<strong>-v</strong> [<em>yes|no</em>]
</dt>
<dd>
<p>
be verbose (default: no)
</p>
</dd>
<dt class="hdlist1">
<strong>-help</strong> 
</dt>
<dd>
<p>
display help and exit
</p>
</dd>
<dt class="hdlist1">
<strong>-version</strong> 
</dt>
<dd>
<p>
display version information and exit
</p>
</dd>
</dl></div>
</div>
</div>
<div class="sect1">
<h2 id="_reporting_bugs">REPORTING BUGS</h2>
<div class="sectionbody">
<div class="paragraph"><p>Report bugs to <a href="https://github.com/genometools/genometools/issues">https://github.com/genometools/genometools/issues</a>.</p></div>
</div>
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